Abstract: Objective Ecological clean small watersheds in the northern mountainous areas of Beijing are critical to the ecological security of the capital. However, there is currently a lack of systematic and comprehensive evaluation of their effectiveness. Methods This study focuses on the Xizhazi small watershed (Huairou District), Hexia small watershed (Miyun District), and Furenxinzhuang small watershed (Changping District), all of which were initiated and implemented in 2021. A comprehensive benefit evaluation system was established, comprising four criterion layers—water quality improvement, ecology, economy, and society—and 13 specific indicators. The Analytic Hierarchy Process (AHP) was employed to determine indicator weights, while the weighted comprehensive index method was used to quantify the changes in benefits before and after management. Furthermore, an obstacle degree model was introduced to diagnose the key factors constraining the sustainable development of these small watersheds. Results The results indicated that the comprehensive benefits of the three small watersheds improved following management, with increases of 19%, 16%, and 8% for Xizhazi, Hexia, and Furenxinzhuang, respectively, all reaching the "primary system" standard. The contribution of subsystems followed the order: water quality improvement > ecology > economy > society, reflecting a management paradigm characterized by water environment enhancement and soil and water conservation as the core drivers. Obstacle diagnosis revealed that: 1) within the ecological subsystem, forest and grass coverage requires prioritized attention; 2) in the economic subsystem, efforts should be directed toward improving the economic input-output ratio and land productivity; 3) in the social subsystem, the Engel coefficient and the proportion of rural employees are the primary constraints; and 4) the water quality subsystem necessitates continued control of Chemical Oxygen Demand (COD).Conclusions This study validates the applicability of the developed evaluation system in the northern mountainous areas of Beijing. The management of ecological clean small watersheds has effectively alleviated regional water environmental pressure and promoted the rational utilization of water and soil resources alongside the enhancement of ecosystem service quality. Future governance should further incentivize farmer participation in maintenance and management, strengthen the promotion of eco-agricultural technologies, and optimize industrial structures to achieve a synergistic win-win for ecological protection and community development.